The proposed new structure also splits the department into a partnership arm and a conservation services arm.
Green Party Conservation spokeswoman Eugenie Sage said the new model would leave DoC "conflicted".
"One part will be trying to exploit our public conservation land while the other is trying to protect it," she said.
"Splitting DoC into a commercial and community 'partnership' arm and a conservation 'services' arm means fewer resources focused on conservation of our protected areas."
Forest & Bird said it was concerned the protection of unique species and places would suffer once the job cuts had been implemented.
Today's announcement followed the loss of hundreds of jobs since 2009, when the government began cutting $13.5 million a year from the department's annual budget, advocacy manager Kevin Hackwell said.
"While fewer jobs have been lost than originally planned, DoC will still be losing many skilled and experienced frontline staff," he said.
However, the Public Service Association, which represents about 1400 DoC staff said while it was disappointed the department was moving ahead with a major restructure, a last-minute funding boost had lessened the impact of planned job losses.
"The eleventh-hour funding allocation has certainly allowed DoC to soften its original proposal but you have to wonder why, when the government is giving over $150 million to tourism, it can't give DoC an even bigger boost which would stop job cuts altogether, PSA national secretary Brenda Pilott said.
She said there was a lot of concern that public access at a number of visitor centres and smaller offices would be restricted by job cuts, "so it's good to see a number of administration and support positions being reinstated".
It would be working with DoC over the coming months to help affected staff make decisions about their future, Ms Pilott said.
The restructure would also see a decrease to the department's 11 conservancy districts into six new conservation delivery regions.
The changes would come into effect by September.